We report a novel mitochondrial DNA alteration in a 12-year-old boy with myopathy. We identified a single nucleotide insertion (an adenine) in the mitochondrial tRNA-glutamine gene. This addition of an additional adenine in a polyadenine stretch (at mitochondrial DNA positions 4366-4369), alters the length of the evolutionary conserved anticodon loop from seven to eight bases. The nt-4370 addition was heteroplasmic and was abundant in the patient's muscle. Lower proportions of mutated mitochondrial DNA were observed in skin fibroblasts, but were below detectable levels in white blood cells. A muscle biopsy of the patient showed ragged red fibers and an unusually high percentage of cytochrome c oxidase-deficient fibers (89%). The pathogenicity of the mutation was also evident by the fact that fibers harboring lower levels of the mutation showed normal cytochrome c oxidase activity. The insertion in the anticodon loop of tRNA(Gln) gene identified in our patient may provide a unique tool to study protein synthesis in human mitochondria.